8S6V: G2D11

Crystal structure of Fab-2D9 chimera complexed to a bis-Tn glycopeptide. Determined by X-ray diffraction at 1.95 Å resolution. Released 25 Jun 2025.

Method: X-ray diffraction
Resolution: 1.95 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 7,355
Mol. weight: 98.1 kDa
Ligands: A2G
Released: 25 Jun 2025

Explore 8S6V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8S6V contains 36 α-helices and 89 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-52	8	2
β-strand	56A-59	4	2
α-helix	61-63	3
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-94	7	2
β-strand	102-103	2	2
β-strand	107-111	5	2
α-helix	114-116	3
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-171	3	4
β-strand	174-184	11	4
α-helix	185-187	3
β-strand	194-199	6	5
α-helix	200-202	3
β-strand	204-209	6	5

Chain B: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	30-30A	2	8
β-strand	30F-31	2	8
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-106	5	7
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-155	3	11
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-187	5
β-strand	191-197	7	11
β-strand	205-210	6	11

Chain C: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
α-helix	7-9	3
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	34-39	6	13
β-strand	45-52	8	13
β-strand	56A-59	4	13
α-helix	61-63	3
β-strand	64	1	12
β-strand	67-72	6	12
α-helix	73-75	3
β-strand	77-82	6	12
α-helix	84-86	3
β-strand	88-94	7	13
β-strand	102-103	2	13
β-strand	107-111	5	13
α-helix	114-116	3
β-strand	117	1	14
α-helix	118-119	2
β-strand	120-124	5	15
β-strand	135-145	11	15
β-strand	146	1	14
β-strand	151-154	4	16
α-helix	155-157	3
β-strand	163-165	3	15
α-helix	166-168	3
β-strand	169-171	3	15
β-strand	174-184	11	15
β-strand	194-199	6	16
α-helix	200-202	3
β-strand	204-209	6	16

Chain D: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	30-30A	2	19
β-strand	30F-31	2	19
β-strand	33-38	6	18
β-strand	45-49	5	18
β-strand	53-54	2	18
α-helix	55	1
β-strand	62-67	6	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	85-90	6	18
α-helix	96	1
β-strand	97-98	2	18
β-strand	102-106	5	18
β-strand	111	1	20
β-strand	114-118	5	21
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	21
β-strand	140	1	20
β-strand	145-150	6	22
β-strand	153-155	3	22
β-strand	159-163	5	21
α-helix	164-167	4
β-strand	173-182	10	21
α-helix	183-187	5
β-strand	191-197	7	22
β-strand	205-210	6	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G2D11 (vh-CH1)	A, C	protein	216	Mus musculus
2D9 (vl-cl)	B, D	protein	217	Mus musculus
Mucin-1 subunit alpha	M, N	protein	10	Homo sapiens	P15941 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8S6V_1 G2D11 (VH-CH1) (chains A, C)
QVQLQQSDAELVKPGASVKISCKASGYIFADHAIHWVKRKPEQGLEWIGYISPGNDDIKY
NEKFKGKATLTADKSSSTAYMQLNSLTSEDSAVYFCKRSLPGTFDYWGQGTTLTVSSAKT
TPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYT
LSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP

Sequence of entity 2 (B, D), FASTA

>8S6V_2 2D9 (VL-CL) (chains B, D)
DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSSDQKNYLAWYQQKPGQSPKLLIYWASTR
ESGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCQQCYSYPFTFGSGTKLERKRADAAPT
VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYS
MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR

Sequence of entity 3 (M, N), FASTA

>8S6V_3 Mucin-1 subunit alpha (chains M, N)
APGSTAPPAX

Ligands and cofactors

ID	Name	Formula	Copies
A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	C8 H15 N O6	4

Water and common crystallization additives (SO4, EDO) are not listed.

Primary citation

Recognizing Tn and STn Epitopes in Protein Context: Structural Advances in Phage Display Libraries for Tumor-Specific Antibody Discovery. Hurtado-Guerrero, R., Gatos, S., Gines-Alcober, I. et al. Nat Chem Biol (2025).

Other PDB entries of the same protein (UniProt P15941 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BSC 1.3 Å, Crystal structure of the Mucin-1 SEA domain
7V64 1.56 Å, Crystal structure of Antibody 16A in complex with MUC1 Glycopeptide(GlycoT)
6BSB 1.6 Å, Crystal structure of the Mucin-1 SEA domain, L1105M mutant, Selenium-derivative
6FZQ 1.7 Å, Crystal structure of scFv-SM3 in complex with compound 3
8S6K 1.75 Å, Crystal structure of ScFv-G2D11 complexed to a bis-Tn glycopeptide
6KX1 1.77 Å, Crystal structure of SN-101 mAb in complex with MUC1 glycopeptide
6FZR 1.8 Å, Crystal structure of scFv-SM3 in complex with compound 2
8AXH 1.85 Å, Crystal structure of a MUC1-like glycopeptide containing the unnatural…
8S6T 1.85 Å, Crystal structure of Fab-3F1 complexed to a bis-STn glycopeptide
1SM3 1.95 Å, Crystal structure of the tumor specific antibody SM3 complex with its peptide epitope
5T6P 1.97 Å, Crystal structure of therapeutic mAB AR20.5 in complex with MUC1 peptide
6TGG 2.0 Å, scFv-1SM3 in complex with glycopeptide containing an sp2-imino sugar

Browse structure collections

About this viewer

MolViewer shows 8S6V directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.